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- PDB-170d: SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLAS... -

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Entry
Database: PDB / ID: 170d
TitleSOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT
ComponentsDNA/RNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*T)-R(P*CAR)-D(P*GP*CP*G)-3')
KeywordsDNA
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsSchweitzer, B.I. / Mikita, T. / Kellogg, G.W. / Gardner, K.H. / Beardsley, G.P.
CitationJournal: Biochemistry / Year: 1994
Title: Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement.
Authors: Schweitzer, B.I. / Mikita, T. / Kellogg, G.W. / Gardner, K.H. / Beardsley, G.P.
History
DepositionMar 14, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA/RNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*T)-R(P*CAR)-D(P*GP*CP*G)-3')
B: DNA/RNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*T)-R(P*CAR)-D(P*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3592
Polymers7,3592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 6
Representative

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*T)-R(P*CAR)-D(P*GP*CP*G)-3')


Mass: 3679.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1
Details: STRUCTURES WERE GENERATED IN THE FOLLOWING MANNER: RESTRAINED MOLECULAR DYNAMICS WAS PERFORMED WITH EXPERIMENTAL DISTANCE AND DIHEDRAL RESTRAINTS GENERATED FROM NOESY AND COSY NMR DATA. ...Details: STRUCTURES WERE GENERATED IN THE FOLLOWING MANNER: RESTRAINED MOLECULAR DYNAMICS WAS PERFORMED WITH EXPERIMENTAL DISTANCE AND DIHEDRAL RESTRAINTS GENERATED FROM NOESY AND COSY NMR DATA. THREE STRUCTURES WERE GENERATED STARTING FROM CANONICAL A-TYPE DNA AND THREE STRUCTURES STARTING FROM CANONICAL B-TYPE DNA. FOR BOTH CONTROL AND ARAC STRUCTURES, THE RMSD OF THE SIX STRUCTURES WAS < 0.7 ANGSTROM. THE SIX STRUCTURES WERE AVERAGED, MINIMIZED AND REFINED USING RELAXATION MATRIX REFINEMENT IN A DYNAMICAL SIMULATED ANNEALING PROTOCOL. THE X-PLOR DISTANCE CONSTRAINT AND SUGAR DIHEDRAL CONSTRAINT TABLES USED IN THE RESTRAINED MOLECULAR DYNAMICS CALCULATIONS FOR THE ARAC-CONTAINING DODECAMER ARE AVAILABLE FROM THE PROTEIN DATA BANK AS A SEPARATE ENTRY.
NMR ensembleConformers calculated total number: 6 / Conformers submitted total number: 1

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